Malaria, with its great biological and social complexity, remains one of the most important global health problems today. One novel approach for controlling infectious diseases is targeting genes responsible for vector competence. The genome of the most efficient malaria vector, Anopheles gambiae, has a number of chromosomal polymorphisms linked to specific adaptations related to malaria transmission. The 2La polymorphic inversion is widespread important phenotypes: decreased Plasmodium falciparum infection rates and adaptation to arid climate. We propose a model where the alternative chromosomal arrangements of the 2La inversion affect vector competence and adaptation to aridity by capturing and stabilizing different haplotypic variants containing allelic complexes of specific genes. Our ability to control these "effector genes" would lead to interference with parasite development and, as a result, to elimination of malaria transmission. The long-term goal of this research is to understand the mechanism of association between inversion polymorphism and the epidemiologically important phenotypes in order to develop novel tools for inhibiting parasite transmission. A recent genetic survey of natural populations of A. gambiae in Mali has identified the strongest P. falciparum resistance loci cluster in a small region near the 2La proximal breakpoint. We hypothesize that i) there are unusually high levels of structural divergence between the 2L arm arrangements in the resistance cluster region, and ii) that genetic variation in the resistance cluster, including adaptive variation for APL1 and/or other immunity-related genes, influences malaria susceptibility and, therefore, physiological vector competence in nature. Similarly, allelic differentiation between the 2L arrangements could be responsible for association of the inversion polymorphism with adaptations to aridity. The major thrust of this exploratory R21 project is to perform detailed comparative analysis of the Plasmodium resistance island in inverted and standard arrangements from wild mosquitoes in order to identify differences in coding sequences. Using targeted resequencing with new, ultra-fast sequencing tools will provide novel methodology for the discovery of genome sequence and structure in wild populations. Our study of the genomic segments obtained from the inverted arrangements will, for the first time, provide for gene annotation over an extensive and epidemiologically significant chromosomal region in wild, non-colonized A. gambiae from a natural population. The specific aims are to: 1) Obtain ~1.5-2 Mb of haploid DNA sequences at both breakpoints of 2La and 2L+ arrangements from wild A. gambiae mosquitoes collected in Mali. 2) Annotate predicted coding sequences in 2La and 2L+ chromosomes, perform comparative genomic analysis of both sequence arrangements, and identify candidate genes for vector competence and ecological adaptation. PUBLIC HEALTH RELEVANCE: Malaria, with its great biological and social complexity, remains one of the most important global health problems today. The proposed research will identify candidate genes for vector competence. Our ability to control genes responsible for interference with parasite development will lead to the elimination of malaria transmission.